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- PDB-5n89: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE GNSFDDWLASKG -

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Basic information

Entry
Database: PDB / ID: 5n89
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE GNSFDDWLASKG
Components
  • GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
  • Streptavidin
Keywordsbiotin binding protein / STREPTAVIDIN / HPQ MOTIF / STREPTAVIDIN PEPTIDE 11101 COMPLEX
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsLyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J.
CitationJournal: Sci Rep / Year: 2017
Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target.
Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
D: Streptavidin
E: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
F: Streptavidin
G: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
H: Streptavidin
I: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
J: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
K: Streptavidin
L: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
M: Streptavidin
N: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
O: Streptavidin
P: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,89724
Polymers161,16016
Non-polymers7378
Water19,9611108
1
A: Streptavidin
B: Streptavidin
C: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
D: Streptavidin
E: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
F: Streptavidin
G: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
I: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,94912
Polymers80,5808
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15160 Å2
ΔGint-87 kcal/mol
Surface area20920 Å2
MethodPISA
2
H: Streptavidin
J: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
K: Streptavidin
L: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
M: Streptavidin
N: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
O: Streptavidin
P: GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,94912
Polymers80,5808
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-85 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.310, 58.305, 88.285
Angle α, β, γ (deg.)104.38, 91.03, 88.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Streptavidin /


Mass: 18849.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide
GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2


Mass: 1295.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Potassium chloride 0.1M HEPES pH 7.5 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.27→85.51 Å / Num. obs: 273857 / % possible obs: 97 % / Redundancy: 1.74 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.71
Reflection shellRedundancy: 1.7 % / CC1/2: 0.378 / Rsym value: 0.9 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→85.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.36 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20373 14193 4.9 %RANDOM
Rwork0.18024 ---
obs0.18141 273857 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å21.24 Å20.71 Å2
2---0.52 Å2-0.12 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.27→85.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 48 1108 9140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.028418
X-RAY DIFFRACTIONr_bond_other_d0.0020.027199
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.89411557
X-RAY DIFFRACTIONr_angle_other_deg0.907316693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78751133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63924.157356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.928151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8531532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021886
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5361.3464328
X-RAY DIFFRACTIONr_mcbond_other1.5351.3464327
X-RAY DIFFRACTIONr_mcangle_it1.9332.0075403
X-RAY DIFFRACTIONr_mcangle_other1.9362.0075404
X-RAY DIFFRACTIONr_scbond_it1.6871.5534090
X-RAY DIFFRACTIONr_scbond_other1.6861.5544090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0152.2126113
X-RAY DIFFRACTIONr_long_range_B_refined2.94116.7989378
X-RAY DIFFRACTIONr_long_range_B_other2.69116.0559166
X-RAY DIFFRACTIONr_rigid_bond_restr1.51315617
X-RAY DIFFRACTIONr_sphericity_free23.8245803
X-RAY DIFFRACTIONr_sphericity_bonded7.906515705
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 1046 -
Rwork0.437 19881 -
obs--95.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2932-0.0527-0.09150.12060.00230.08-0.0122-0.02360.00280.01280.0078-0.00940.00110.01920.00450.0341-0.0299-0.01920.05850.00240.02122.5587-3.3965-178.9054
20.3854-0.13470.03130.2396-0.05640.01930.01630.03740.10080.0082-0.0193-0.05130.0026-0.00030.0030.0354-0.0307-0.01050.05010.01350.04723.375116.3467-185.3185
32.7962-0.0513-0.62450.11190.2740.81440.00070.0817-0.063-0.0253-0.026-0.0135-0.0466-0.0440.02530.0332-0.01060.00530.07150.03740.04486.001212.6017-200.3623
40.4693-0.15010.01640.15390.01120.05340.03170.0387-0.10710.0132-0.01590.0390.01520.0098-0.01590.038-0.0283-0.02140.0464-0.00190.037311.2107-14.4968-184.9981
52.21850.016-0.54640.1996-0.20640.34740.07960.1888-0.07620.0149-0.07510.0392-0.05080.017-0.00440.05740.0063-0.04290.1181-0.04650.0518.5683-11.0515-199.9514
60.3027-0.1301-0.01830.2309-0.00140.08330.0024-0.013-0.00370.0110.00880.0189-0.0032-0.0227-0.01110.0319-0.0315-0.01260.0670.00220.0192-8.08825.2418-179.1178
70.13160.0741-0.35213.096-0.32720.994-0.028-0.0283-0.0199-0.0513-0.0335-0.13770.0720.01220.06150.0393-0.0089-0.00630.1030.0050.0128-4.47662.8036-163.8833
80.3464-0.2499-0.09060.2812-0.01280.1831-0.02150.02360.00640.0250.0033-0.03330.00710.01310.01820.0315-0.0275-0.01750.0751-0.00410.022851.0633-18.4733-219.6496
91.63520.89330.72372.01360.78941.97790.005-0.13150.03350.0922-0.05910.01780.0549-0.05550.05410.0435-0.024-0.01790.0733-0.00440.01518.9019-0.4039-163.9116
100.3309-0.5703-0.44723.0167-1.23782.607-0.0051-0.03460.0167-0.02870.12070.08140.02090.0148-0.11560.0464-0.0316-0.03180.06710.0020.035147.2499-5.8494-210.358
110.512-0.2725-0.08170.3231-0.04240.0622-0.06060.0147-0.15330.04850.02490.0790.0069-0.01490.03580.043-0.02850.01250.0540.00320.059339.9141-30.8262-216.1582
128.1998-1.5374-1.73970.67140.93971.4127-0.12130.3778-0.1045-0.01010.00030.08050.0235-0.03520.1210.0482-0.0617-0.01530.1093-0.01780.077637.3834-38.6756-229.4972
130.5191-0.1362-0.17980.1043-0.03280.16980.030.1175-0.0440.0197-0.03580.0139-0.028-0.06730.00580.0311-0.0219-0.01450.1149-0.01460.02520.1265-12.6887-225.3461
140.18950.3569-0.67792.1908-1.04852.70670.0056-0.0049-0.01020.1193-0.07760.0167-0.09360.10080.07210.0404-0.0285-0.01270.072-0.00410.011723.6989-4.2532-212.6878
150.5036-0.1968-0.22640.10580.06170.14710.10240.1960.0115-0.0213-0.0947-0.0174-0.0502-0.0782-0.00760.04610.0071-0.01260.14340.00980.017231.3694-8.9559-237.4667
161.65350.2298-0.47060.17760.17020.52090.03460.1061-0.0852-0.0001-0.0506-0.0162-0.0218-0.1090.0160.02620.0004-0.02190.1723-0.02310.024634.5447-21.641-245.7024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 134
2X-RAY DIFFRACTION2B14 - 135
3X-RAY DIFFRACTION3C1 - 13
4X-RAY DIFFRACTION4D14 - 135
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F14 - 135
7X-RAY DIFFRACTION7G1 - 13
8X-RAY DIFFRACTION8H14 - 135
9X-RAY DIFFRACTION9I1 - 13
10X-RAY DIFFRACTION10J1 - 13
11X-RAY DIFFRACTION11K16 - 134
12X-RAY DIFFRACTION12L2 - 13
13X-RAY DIFFRACTION13M14 - 135
14X-RAY DIFFRACTION14N1 - 13
15X-RAY DIFFRACTION15O15 - 134
16X-RAY DIFFRACTION16P1 - 13

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